6YUT
Structure of recombinant human beta-glucocerebrosidase in complex with N-acyl functionalised cyclophellitol aziridine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NT0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.03 M KCl, 0.1 M sodium acetate pH 4.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.699 | α = 90 |
b = 285.525 | β = 90 |
c = 91.902 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 X 16M | 2016-01-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.979490 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 1.76 | 47.633 | 99.8 | 0.098 | 0.042 | 0.997 | 10 | 6.3 | 143462 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.76 | 1.79 | 99.9 | 0.845 | 0.37 | 0.835 | 1.7 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2NT0 | 1.76 | 47.633 | 143436 | 7160 | 99.7 | 0.184 | 0.183 | 0.2084 | 31.049 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
5.597 | -2.895 | -2.702 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.051 |
r_dihedral_angle_4_deg | 20.04 |
r_dihedral_angle_3_deg | 13.978 |
r_dihedral_angle_1_deg | 7.202 |
r_lrange_it | 6.016 |
r_lrange_other | 6.016 |
r_dihedral_angle_other_1_deg | 4.82 |
r_scangle_it | 4.192 |
r_scangle_other | 4.192 |
r_mcangle_it | 2.913 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7808 |
Nucleic Acid Atoms | |
Solvent Atoms | 735 |
Heterogen Atoms | 314 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
Aimless | data scaling |
MOLREP | phasing |